Why dna is double helix?

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DNA Double helix structure
Source: nationalgeographic.com

DNA is Double Helix

Erwin Chargaff and his colleagues at Columbia University in 1940’s observed that four bases in DNA occur in definite proportions and concluded:

  • DNA specimen isolated from different tissues of the same species has the same base composition.
  • The base composition of DNA varies from one species to another.
  • The base composition of DNA in a given species doest not change with the age of organism, its nutritional status, or change in environmental conditions.
  • The number of adenine residues in all DNA’s regardless of the species is equal to the number of thymine residues (i.e. A=T), and the number of guanine residues is equal to the number of cytosine residues (C=G). This led to Chargaff’s rule.
  • We find in the above table that the amount of A in yeast is nearly equal to T, the slight error may be an experimental one.

In 1953, nearly 20 years after James Watson and Francis Crick gave the three dimensional modal for DNA using Chargaff’s rule and X-Ray diffraction studies made by Rosalind Franklin and Mauric Wilkins. In 1962, Watson, Crick and Wikins got Nobel’s prize for elucidating the structure of DNA.

Watson and Crick -DNA Model

DNA model as proposed by Watson and Crick

  • Two right handed helical polynucleotide chains are coiled around a common axis and are running in opposite direction.
  • The purine and pyrimidine bases are on the inside of the helix, whereas phosphate and deoxyribose units are on the outside. The plane of the bses is perpendicular to the axis. The planes of the sugar are nearly at right angle to those of the bases.
  • The diameter of helix is 20Ao. Adjacent bases are separated by 3.4Ao along the helix axis and related by a rotation of 36o. The helical structure repeats after every ten residues on each chain i.e. at an interval of 34Ao.
  • Two chain are held together by hydrogen bond between pair of bases. Adenine is always paired with thymine and guanine with cytosine.
hydrogen bonding between adenine and thymine
Hydrogen bonding between adenine and thymine
hydrogen bonding between cytosine and guanine
Hydrogen bonding between cytosine and guanine

The Watson-Crick model is also referred to as B-DNA. This form of the DNA is the most stable structure for random sequences. DNA can occur in three different conformations. Two other variant DNA structures, that have been well characterized in crystal structures, are the A and Z-DNA.

Watson and Crick model of DNA
Watson and Crick model of DNA

Types of DNA

A-DNA: It is a favored DNA structure in many solutions that are relatively devoid of water. It is right handed helical structure with rise in base pairs 2.3Ao and number of bases per helical turn in 11. It is shorter and thicker than B-DNA and has a central hole.

Z-DNA. Unlike B and A-DNA, Z-DNA is left handed and has 12 base pairs per turn, the rise in base pairs is 3.8Ao. This type of DNA is observed when there is repeated sequence of C and G. This repeat leads to Zigzag DNA.

Palindrome sequences: Sometime in DNA the base sequence on one strand repeats on the other strand or invert repeat, is called palindrome sequence as shown. They have two-fold axis of symmetry. They are the important points of attack by restriction endonucleases in DNA molecules.

palindrome sequences
Palindrome sequences

Forces Stabilizing the DNA

Covalent bonds, of course, are important to provide glue that links atom in molecule but weak forces are equally important i.e. hydrophobic, Vander Waal, hydrogen bonds, and electrostatic interactions.

  • The hydrophobic purine and pyrimidine rings of the bases are forced into the center of double helix whereas, the hydrophilic substituents of bases are exposed to the solvent in the grooves.
  • The stacked bases, form Vander Waals contacts. Although these are very weak forces, becomes very important for the stability of DNA when their number is large i.e. more than 104 base pairs.
  • The base pairs are hydrogen bonded i.e. G=C and A=T in which the former is more stable than the latter, as the number of hydrogen bonds is three to two.
  • DNA is highly negatively charged due to phosphodiester linkage in the backbone at pH=7.0. They stabilized by cellular anions, Mg++.

Double helix can unwind

DNA double helix can unwind locally during process such as DNA replication transcription, and genetic recombination. Complete unwinding of DNA can occur in vitro by heating or by adding organic solvent or high salt concentration, and this process leads to denaturation of DNA. It is also called as helix to coil transition. This is due to the breakage of Hydrogen bonding between bases. It has been observed that when DNA is totally unwound, it absorbs 37% more light at 270nm than in native form. The temperature at which half of DNA is unwound, it is termed as its melting temperature Tm. The DNA with higher content of G=C pairs has higher Tm. The organism living at thermophilic temperature has high content of GC and hence high Tm. When denatured DNA is slowly cooled, the two complementary strands join to form double helix, the process is called annealing or hybridization. It occurs only in complementary polynucleotide chains.

Double helix unwind
The synthesis of RNA on a DNA template. (a) The DNA double helix with 10 labeled base pairs. (b) The two strands of the helix unwind; note that only one of the strands is used as the template for RNA synthesis. (c) A short length of RNA (shown in red) is being synthesized: a nucleotide with base A is about to be added to the RNA strand. In reality, the RNA molecule would be much longer than the chain of nine nucleotides shown here.

Nucleases

Enzymes that hydrolyze the phosphodiester bond of nucleic acids are collectively known as nucleases. They are ubiquitous in nature i.e. found in the cells of all the organisms. They can be specifically classified as

Nucleases that are specific for RNA – – – Ribonucleases/RNases

Nucleases that are specific for DNA – – – Deoxyribonucleases/ DNases

Nucleases are further classified on the basis of point of their attack. Those attack on the 5’ or 3’ ends of nucleic acids are termed as exonucleases, whereas those attack within the molecule are termed as endonucleases. Nucleases that yield, nucleoside 3’-monophosphate on attack are termed as (b) type endonucleases, whereas that yield nucleoside 5’-monophosphate are (a) type endonucleases.

Endonucleases may have specificity which varies for different base sequences.

Some endonucleases hydrolyze between any nucleotides.

Some hdrolyze preferentially at purine or pyrimidine nucleotide.

Some cleave only at specific sequences, also called restriction endonucleaases.

The term restriction endonucleases derived originally from the observation that certain bacteria can block infection of a particular viruses by destroying the incoming viral DNA. Bacteria that posses this activity, are called restricting hosts. The viruses that are capable of establishing in the host cell contains modified bases in their DNA (i.e. methylated at specific bases). The restriction endonucleases cleave any DNA that is unmethylated at these sites, but the methylated DNA is not degraded. These enzymes cut the DNA at palindrome sites.

DNA as a Genetic Material

No doubt the DNA is the genetic material of almost all the living organisms. The nature has opted this molecule, being more stable than the RNA. It is so stable that scientist are cloning the DNA from fossils of Dinosaurs. This stability is due to the absence of hydroxyl group at 2’ position of pentose sugar. This hydroxyl group at the 2’ position in RNA makes it vulnerable to alkali attack. Some of the viruses have RNA as genetic material. It is beyound doubt that RNA came earlier than DNA.

RNA- Ribonucleic Acid

Unlike the DNA, the RNA molecules are single stranded, but may form in some regions, the secondary structures, by folding it self to form double helix. In this molecule, the A base pairs with U, as T is absent. The double stranded helix of RNA is vary similar to A-DNA structure.

Such hair pin structures play an important role in recognition of RNA molecules by different enzymes. Based on cellular location and functions they have been put into three main classes.

  • r-RNA (’r’ stands for ribosomal as chief constituents of ribosomes)
  • t-RNA (’t’ stands for transfer, i.e. they transfer amino acids from soluble fraction of cytosol by acting as adaptor molecule to the ribosomes, the site for proteins synthesis.
  • m-RNA (’m’ stands for messenger, i.e. they take message from the DNA (storehouse of genetic information) to the site of protein synthesis (ribosome).
  • The eukaryotic cells contain other hn-RNA i.e. heteronuclear, RNA molecules that are the precursor of m-Rna and Sn-RNA (small nuclear) molecules that are involved in RNA processing, along with the proteins.

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